Spatial and temporal dynamics of West Nile virus between Africa and Europe

It is unclear whether West Nile virus (WNV) circulates between Africa and Europe, despite numerous studies supporting an African origin and high transmission in Europe. We integrated genomic data with geographic observations and phylogenetic and phylogeographic inferences to uncover the spatial and temporal viral dynamics of WNV between these two continents. We focused our analysis towards WNV lineages 1 (L1) and 2 (L2), the most spatially widespread and pathogenic WNV lineages. Our study shows a Northern-Western African origin of L1, with back-and-forth exchanges between West Africa and Southern-Western Europe; and a Southern African origin of L2, with one main introduction from South Africa to Europe, and no back introductions observed. We also noticed a potential overlap between L1 and L2 Eastern and Western phylogeography and two Afro-Palearctic bird migratory flyways. Future studies linking avian and mosquito species susceptibility, migratory connectivity patterns, and phylogeographic inference are suggested to elucidate the dynamics of emerging viruses.


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March 2021

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Field-specific reporting
Please select the one below that is the best fit for your research. If you are not sure, read the appropriate sections before making your selection. The code used in the analyses is available at https://github.com/andrea-silverj/WNV-Afr_Eur/tree/main/scripts (DOI: https://zenodo.org/ badge/latestdoi/611814462). Assembly was automatically performed at the end of the sequencing run using the 'National Reference In this study we used genome sequences obtained from the National Surveillance plan in ltaly and Senegal other than public available sequences downloaded from NCBI. The sequence dataset included in this study was used to perform phylogenetic and phylogeographic analyses aimed at uncovering the viral dynamics of West Nile virus between Africa and Europe.
Sequences were obtained from samples collected in In ltaly between 2001 and 2022 as part of the National Surveillance plan coordinated by the Ministry of Health, the Istituto Superiore di Sanità (epidemiology and national reference laboratory, human), and the Istituto Zooprofilattico of Abruzzo and Molise (IZS-Teramo) (epidemiology and national reference laboratory, animal/entomology) (https://westnile.izs.it/j6_wnd/home, https://www.epicentro.iss.it/westnile/) and in Senegal, where sample activities were carried out between 1988 and 2022 by the lnstitut Pasteur de Dakar (IPD-Dakar) in collaboration with the Ministry of Health, within the framework of the mosquito-based arbovirus surveillance system and a sentinel syndromic surveillance network (4S). All samples collected in Italy and Senegal were screened by real time PCR for West Nile virus (WNV). Positive samples were sequenced and all newly obtained complete genome sequences, representing the viral WNV population in Italy and Senegal, were considered in this study. Moreover, we retrieved all the WNV available genomes from the NCBI genbank database. All the data and their source are accurately described in Supplementary Tables 1 and 2, as reported in the "Data Availability" statement.
The samples used in this study were previously collected in ltaly as part of the National Surveillance plan coordinated by the Ministry of Health, the Istituto Superiore di Sanità (epidemiology and national reference laboratory, human), and the Istituto Zooprofilattico of Abruzzo and Molise (IZS-Teramo) (epidemiology and national reference laboratory, animal/entomology) (https://westnile.izs.it/ j6_wnd/home, https://www.epicentro.iss.it/westnile/), and in Senegal by the lnstitut Pasteur de Dakar (IPD-Dakar) in collaboration with the Ministry of Heal within the framework of the mosquito-based arbovirus surveillance system and a sentinel syndromic surveillance network (4S).
The samples chosen for this study were all newly generated WNV genome sequences obtained at IZS-Teramo and IPD-Dakar plus all public avaiable WNV NCBI genome sequences. As the minimum sample size for performing tree inference is 4 sequences, and the size of our samples was always greater than 150, the number of samples was more than sufficient to perform a robust phylogenetic and phylogeographic analysis.
In Italy, the cases reported in this study were investigated with routine procedures according to the national surveillance plan for arbovirus infection (2020-2025). The integrated surveillance plan is coordinated by the Ministry of Health, the Istituto Superiore di Sanità (epidemiology and national reference laboratory, human), and the Istituto Zooprofilattico of Abruzzo and Molise (IZS-Teramo) (epidemiology and national reference laboratory, animal/entomology) (https://westnile.izs.it/j6_wnd/home, https:// www.epicentro.iss.it/westnile/), which perform a coordinated mosquito, human, and animal surveillance. In Senegal, an human surveillance system, coupled with a mosquito-based arbovirus surveillance system, has been set up by the Institut Pasteur de Dakar in collaboration with the Ministry of Health, carrying out a monthly screening of arbovirus and hemorhagic fever virus samples. All data are recorded on scientific laboratory notebooks and computer databases by the WHO collaborating center for arboviruses and hemorhagic fever viruses (CRORA), and reported in specific platforms of the Ministry of Health.
AII samples were collected in ltaly between 2008 and 2022 under the National Surveillance plan. Each year, seasonal surveillance activities are defined on the basis of the previous year's virus circulation (risk areas), while any WNV detection in birds, mosquitoes, equids, and humans triggers the activation of prevention measures (blood and transplant measures including nucleic acid testing, vector control, and risk communication campaigns aimed at citizens). Therefore, the start date of these measures can vary each year and, in each province, depending on the viral circulation. Particularly, the surveillance plan includes: i) active surveillance which is made by the fortnightly capture of mosquitoes using a network of fixed traps and the capture of target bird species, and ii) the passive surveillance characterised by the collection of dead-found birds, and by testing cases of neurological disease in horses and viral meningoencephalitis cases in humans. Generally, the active surveillance is performed in high risk regions every year, from the end of April to the beginning of November. In Senegal the samples were collected between 1989 and 2022 by the lnstitut Pasteur de Dakar (IPD-Dakar), from June to December each year, in the Barkédji area (15°17" N, 14°52" W), located in the Sahelian biogeographic domain.
The L1 sequence OP846974.1 and the L2 sequence OK239667.1 were excluded from our phylogenetic analysis, because detected as recombinant The study is fully reproducible by downloading all data from the data repository described in the "Data Availability" statement and by repeating the analyses using the scripts provided in the "Code Availability" statement of our paper.
Randomization is often used in clinical trials while here is not applicable because all genome sequences available on the NCBI database plus the ones obtained from WNV positive samples in Italy and Senegal by the Istituto Zooprofilattico of Abruzzo and Molise and the Institut Pasteur de Dakar were included in the phylogenetic and phylogeographic analyses.
Blinding was not relevant to this study. Our study includes a phylogenetic and phylogeographic analysis and blinding would have no effect on that. In fact, all genome sequences available on the NCBI database plus the ones obtained from WNV positive samples in Italy and Senegal by the Istituto Zooprofilattico of Abruzzo and Molise and the Institut Pasteur de Dakar were included in the final